aiagents4pharma 1.8.3__py3-none-any.whl → 1.9.0__py3-none-any.whl

aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml

@@ -3,4 +3,6 @@ state_modifier: >
   You are Talk2BioModels agent.
   If the user asks for the uploaded model, 
   then pass the use_uploaded_model argument
-    as True.
+  as True. If the user asks for simulation, 
+  then suggest a value for the `simulation_name`
+  argument.

aiagents4pharma/talk2biomodels/__init__.py

@@ -4,4 +4,4 @@ This file is used to import the models and tools.
 from . import models
 from . import tools
 from . import agents
-from . import states
+from . import states

aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py

@@ -20,5 +20,5 @@ class Talk2Biomodels(AgentState):
     # the operator for the sbml_file_path field.
     # https://langchain-ai.github.io/langgraph/troubleshooting/errors/INVALID_CONCURRENT_GRAPH_UPDATE/
     sbml_file_path: Annotated[list, operator.add]
-    dic_simulated_data: dict
+    dic_simulated_data: Annotated[list[dict], operator.add]
     llm_model: str

aiagents4pharma/talk2biomodels/tests/test_langgraph.py

@@ -1,7 +1,8 @@
 '''
-Test cases
+Test cases for Talk2Biomodels.
 '''
 
+import pandas as pd
 from langchain_core.messages import HumanMessage, ToolMessage
 from ..agents.t2b_agent import get_app
 
@@ -13,7 +14,8 @@ def test_get_modelinfo_tool():
     app = get_app(unique_id)
     config = {"configurable": {"thread_id": unique_id}}
     # Update state
-    app.update_state(config,{"sbml_file_path": ["BIOMD0000000537.xml"]})
+    app.update_state(config,
+      {"sbml_file_path": ["aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml"]})
     prompt = "Extract all relevant information from the uploaded model."
     # Test the tool get_modelinfo
     response = app.invoke(
@@ -56,26 +58,70 @@ def test_ask_question_tool():
 
     ##########################################
     # Test ask_question tool when simulation
-    # results are not available
+    # results are not available i.e. the
+    # simulation has not been run. In this
+    # case, the tool should return an error
     ##########################################
     # Update state
     app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    # Define the prompt
     prompt = "Call the ask_question tool to answer the "
     prompt += "question: What is the concentration of CRP "
-    prompt += "in serum at 1000 hours?"
-
-    # Test the tool get_modelinfo
-    response = app.invoke(
-                        {"messages": [HumanMessage(content=prompt)]},
-                        config=config
-                    )
-    assistant_msg = response["messages"][-1].content
-    # Check if the assistant message is a string
-    assert isinstance(assistant_msg, str)
+    prompt += "in serum at 1000 hours? The simulation name "
+    prompt += "is `simulation_name`."
+    # Invoke the tool
+    app.invoke(
+            {"messages": [HumanMessage(content=prompt)]},
+            config=config
+        )
+    # Get the messages from the current state
+    # and reverse the order
+    current_state = app.get_state(config)
+    reversed_messages = current_state.values["messages"][::-1]
+    # Loop through the reversed messages until a
+    # ToolMessage is found.
+    for msg in reversed_messages:
+        # Assert that the message is a ToolMessage
+        # and its status is "error"
+        if isinstance(msg, ToolMessage):
+            assert msg.status == "error"
 
 def test_simulate_model_tool():
     '''
-    Test the simulate_model tool.
+    Test the simulate_model tool when simulating
+    multiple models.
+    '''
+    unique_id = 123
+    app = get_app(unique_id)
+    config = {"configurable": {"thread_id": unique_id}}
+    app.update_state(config, {"llm_model": "gpt-4o-mini"})
+    # Upload a model to the state
+    app.update_state(config,
+        {"sbml_file_path": ["aiagents4pharma/talk2biomodels/tests/BIOMD0000000449_url.xml"]})
+    prompt = "Simulate models 64 and the uploaded model"
+    # Invoke the agent
+    app.invoke(
+        {"messages": [HumanMessage(content=prompt)]},
+        config=config
+    )
+    current_state = app.get_state(config)
+    dic_simulated_data = current_state.values["dic_simulated_data"]
+    # Check if the dic_simulated_data is a list
+    assert isinstance(dic_simulated_data, list)
+    # Check if the length of the dic_simulated_data is 2
+    assert len(dic_simulated_data) == 2
+    # Check if the source of the first model is 64
+    assert dic_simulated_data[0]['source'] == 64
+    # Check if the source of the second model is upload
+    assert dic_simulated_data[1]['source'] == "upload"
+    # Check if the data of the first model contains
+    assert '1,3-bisphosphoglycerate' in dic_simulated_data[0]['data']
+    # Check if the data of the second model contains
+    assert 'mTORC2' in dic_simulated_data[1]['data']
+
+def test_integration():
+    '''
+    Test the integration of the tools.
     '''
     unique_id = 123
     app = get_app(unique_id)
@@ -138,9 +184,9 @@ def test_simulate_model_tool():
     reversed_messages = current_state.values["messages"][::-1]
     # Loop through the reversed messages
     # until a ToolMessage is found.
-    expected_artifact = ['CRP[serum]', 'CRPExtracellular']
-    expected_artifact += ['CRP Suppression (%)', 'CRP (% of baseline)']
-    expected_artifact += ['CRP[liver]']
+    expected_header = ['Time', 'CRP[serum]', 'CRPExtracellular']
+    expected_header += ['CRP Suppression (%)', 'CRP (% of baseline)']
+    expected_header += ['CRP[liver]']
     predicted_artifact = []
     for msg in reversed_messages:
         if isinstance(msg, ToolMessage):
@@ -150,9 +196,14 @@ def test_simulate_model_tool():
             if msg.name == "custom_plotter":
                 predicted_artifact = msg.artifact
                 break
-    # Check if the two artifacts are equal
-    # assert expected_artifact in predicted_artifact
-    assert set(expected_artifact).issubset(set(predicted_artifact))
+    # Convert the artifact into a pandas dataframe
+    # for easy comparison
+    df = pd.DataFrame(predicted_artifact)
+    # Extract the headers from the dataframe
+    predicted_header = df.columns.tolist()
+    # Check if the header is in the expected_header
+    # assert expected_header in predicted_artifact
+    assert set(expected_header).issubset(set(predicted_header))
     ##########################################
     # Test custom_plotter tool when the
     # simulation results are available but

aiagents4pharma/talk2biomodels/tools/ask_question.py

@@ -23,6 +23,8 @@ class AskQuestionInput(BaseModel):
     Input schema for the AskQuestion tool.
     """
     question: str = Field(description="question about the simulation results")
+    simulation_name: str = Field(description="""Name assigned to the simulation
+                                 when the tool simulate_model was invoked.""")
     state: Annotated[dict, InjectedState]
 
 # Note: It's important that every field has type hints.
@@ -39,6 +41,7 @@ class AskQuestionTool(BaseTool):
 
     def _run(self,
              question: str,
+             simulation_name: str,
              state: Annotated[dict, InjectedState]) -> str:
         """
         Run the tool.
@@ -46,18 +49,24 @@ class AskQuestionTool(BaseTool):
         Args:
             question (str): The question to ask about the simulation results.
             state (dict): The state of the graph.
-            run_manager (Optional[CallbackManagerForToolRun]): The CallbackManagerForToolRun object.
+            simulation_name (str): The name assigned to the simulation.
 
         Returns:
             str: The answer to the question.
         """
         logger.log(logging.INFO,
-                   "Calling ask_question tool %s", question)
-        # Check if the simulation results are available
-        if 'dic_simulated_data' not in state:
-            return "Please run the simulation first before \
-                asking a question about the simulation results."
-        df = pd.DataFrame.from_dict(state['dic_simulated_data'])
+                   "Calling ask_question tool %s, %s", question, simulation_name)
+        dic_simulated_data = {}
+        for data in state["dic_simulated_data"]:
+            for key in data:
+                if key not in dic_simulated_data:
+                    dic_simulated_data[key] = []
+                dic_simulated_data[key] += [data[key]]
+        # print (dic_simulated_data)
+        df_simulated_data = pd.DataFrame.from_dict(dic_simulated_data)
+        df = pd.DataFrame(
+                df_simulated_data[df_simulated_data['name'] == simulation_name]['data'].iloc[0]
+                )
         prompt_content = None
         # if run_manager and 'prompt' in run_manager.metadata:
         #     prompt_content = run_manager.metadata['prompt']

aiagents4pharma/talk2biomodels/tools/custom_plotter.py

@@ -6,14 +6,11 @@ Tool for plotting a custom figure.
 
 import logging
 from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
-from typing import Type, List, TypedDict, Annotated, Tuple, Union, Literal
 from pydantic import BaseModel, Field
 import pandas as pd
-import pandas as pd
 from langchain_openai import ChatOpenAI
 from langchain_core.tools import BaseTool
 from langgraph.prebuilt import InjectedState
-from langgraph.prebuilt import InjectedState
 
 # Initialize logger
 logging.basicConfig(level=logging.INFO)
@@ -24,7 +21,7 @@ class CustomPlotterInput(BaseModel):
     Input schema for the PlotImage tool.
     """
     question: str = Field(description="Description of the plot")
-    state: Annotated[dict, InjectedState]
+    simulation_name: str = Field(description="Name assigned to the simulation")
     state: Annotated[dict, InjectedState]
 
 # Note: It's important that every field has type hints.
@@ -41,10 +38,10 @@ class CustomPlotterTool(BaseTool):
     description: str = "A tool to make custom plots of the simulation results"
     args_schema: Type[BaseModel] = CustomPlotterInput
     response_format: str = "content_and_artifact"
-    response_format: str = "content_and_artifact"
 
     def _run(self,
              question: str,
+             simulation_name: str,
              state: Annotated[dict, InjectedState]
              ) -> Tuple[str, Union[None, List[str]]]:
         """
@@ -53,17 +50,24 @@ class CustomPlotterTool(BaseTool):
         Args:
             question (str): The question about the custom plot.
             state (dict): The state of the graph.
-            question (str): The question about the custom plot.
-            state (dict): The state of the graph.
 
         Returns:
             str: The answer to the question
         """
         logger.log(logging.INFO, "Calling custom_plotter tool %s", question)
-        # Check if the simulation results are available
-        # if 'dic_simulated_data' not in state:
-        #     return "Please run the simulation first before plotting the figure.", None
-        df = pd.DataFrame.from_dict(state['dic_simulated_data'])
+        dic_simulated_data = {}
+        for data in state["dic_simulated_data"]:
+            for key in data:
+                if key not in dic_simulated_data:
+                    dic_simulated_data[key] = []
+                dic_simulated_data[key] += [data[key]]
+        # Create a pandas dataframe from the dictionary
+        df = pd.DataFrame.from_dict(dic_simulated_data)
+        # Get the simulated data for the current tool call
+        df = pd.DataFrame(
+                df[df['name'] == simulation_name]['data'].iloc[0]
+                )
+        # df = pd.DataFrame.from_dict(state['dic_simulated_data'])
         species_names = df.columns.tolist()
         # Exclude the time column
         species_names.remove('Time')
@@ -76,7 +80,8 @@ class CustomPlotterTool(BaseTool):
             A list of species based on user question.
             """
             relevant_species: Union[None, List[Literal[*species_names]]] = Field(
-                    description="List of species based on user question. If no relevant species are found, it will be None.")
+                    description="""List of species based on user question.
+                    If no relevant species are found, it will be None.""")
         # Create an instance of the LLM model
         llm = ChatOpenAI(model=state['llm_model'], temperature=0)
         llm_with_structured_output = llm.with_structured_output(CustomHeader)
@@ -90,5 +95,6 @@ class CustomPlotterTool(BaseTool):
         logger.info("Extracted species: %s", extracted_species)
         if len(extracted_species) == 0:
             return "No species found in the simulation results that matches the user prompt.", None
-        content = f"Plotted custom figure with species: {', '.join(extracted_species)}"
-        return content, extracted_species
+        # Include the time column
+        extracted_species.insert(0, 'Time')
+        return f"Custom plot {simulation_name}", df[extracted_species].to_dict(orient='records')

aiagents4pharma/talk2biomodels/tools/get_modelinfo.py

@@ -25,12 +25,12 @@ class RequestedModelInfo:
     """
     Dataclass for storing the requested model information.
     """
-    species: bool = Field(description="Get species from the model.")
-    parameters: bool = Field(description="Get parameters from the model.")
-    compartments: bool = Field(description="Get compartments from the model.")
-    units: bool = Field(description="Get units from the model.")
-    description: bool = Field(description="Get description from the model.")
-    name: bool = Field(description="Get name from the model.")
+    species: bool = Field(description="Get species from the model.", default=False)
+    parameters: bool = Field(description="Get parameters from the model.", default=False)
+    compartments: bool = Field(description="Get compartments from the model.", default=False)
+    units: bool = Field(description="Get units from the model.", default=False)
+    description: bool = Field(description="Get description from the model.", default=False)
+    name: bool = Field(description="Get name from the model.", default=False)
 
 class GetModelInfoInput(BaseModel):
     """

aiagents4pharma/talk2biomodels/tools/simulate_model.py

@@ -52,10 +52,10 @@ class TimeSpeciesNameConcentration:
 class RecurringData:
     """
     Dataclass for storing the species and time data 
-    on recurring basis.
+    on reocurring basis.
     """
     data: List[TimeSpeciesNameConcentration] = Field(
-        description="species and time data on recurring basis",
+        description="species and time data on reocurring basis",
         default=None)
 
 @dataclass
@@ -68,12 +68,15 @@ class ArgumentData:
         description="species name and initial concentration data",
         default=None)
     recurring_data: RecurringData = Field(
-        description="species and time data on recurring basis",
+        description="species and time data on reocurring basis",
         default=None)
+    simulation_name: str = Field(
+        description="""An AI assigned `_` separated name of
+        the simulation based on human query""")
 
 def add_rec_events(model_object, recurring_data):
     """
-    Add recurring events to the model.
+    Add reocurring events to the model.
     """
     for row in recurring_data.data:
         tp, sn, sc = row.time, row.species_name, row.species_concentration
@@ -86,9 +89,12 @@ class SimulateModelInput(BaseModel):
     """
     Input schema for the SimulateModel tool.
     """
-    sys_bio_model: ModelData = Field(description="model data", default=None)
-    arg_data: ArgumentData = Field(description="time, species, and recurring data",
-                                        default=None)
+    sys_bio_model: ModelData = Field(description="model data",
+                                     default=None)
+    arg_data: ArgumentData = Field(description=
+                                   """time, species, and reocurring data
+                                   as well as the simulation name""",
+                                   default=None)
     tool_call_id: Annotated[str, InjectedToolCallId]
     state: Annotated[dict, InjectedState]
 
@@ -153,12 +159,20 @@ class SimulateModelTool(BaseTool):
             interval=interval
             )
 
+        dic_simulated_data = {
+            'name': arg_data.simulation_name,
+            'source': sys_bio_model.biomodel_id if sys_bio_model.biomodel_id else 'upload',
+            'tool_call_id': tool_call_id,
+            'data': df.to_dict()
+        }
+
         # Prepare the dictionary of updated state for the model
         dic_updated_state_for_model = {}
         for key, value in {
-                        "model_id": [sys_bio_model.biomodel_id],
-                        "sbml_file_path": [sbml_file_path],
-                        }.items():
+            "model_id": [sys_bio_model.biomodel_id],
+            "sbml_file_path": [sbml_file_path],
+            "dic_simulated_data": [dic_simulated_data],
+            }.items():
             if value:
                 dic_updated_state_for_model[key] = value
 
@@ -166,11 +180,11 @@ class SimulateModelTool(BaseTool):
         return Command(
                 update=dic_updated_state_for_model|{
                 # update the state keys
-                "dic_simulated_data": df.to_dict(),
+                # "dic_simulated_data": df.to_dict(),
                 # update the message history
                 "messages": [
                     ToolMessage(
-                        content="Simulation results are ready.",
+                        content=f"Simulation results of {arg_data.simulation_name}",
                         tool_call_id=tool_call_id
                         )
                     ],

{aiagents4pharma-1.8.3.dist-info → aiagents4pharma-1.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: aiagents4pharma
-Version: 1.8.3
+Version: 1.9.0
 Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D
 Classifier: Programming Language :: Python :: 3
 Classifier: License :: OSI Approved :: MIT License

{aiagents4pharma-1.8.3.dist-info → aiagents4pharma-1.9.0.dist-info}/RECORD

@@ -4,26 +4,26 @@ aiagents4pharma/configs/config.yaml,sha256=8y8uG6Dzx4-9jyb6hZ8r4lOJz5gA_sQhCiSCg
 aiagents4pharma/configs/talk2biomodels/__init__.py,sha256=5ah__-8XyRblwT0U1ByRigNjt_GyCheu7zce4aM-eZE,68
 aiagents4pharma/configs/talk2biomodels/agents/__init__.py,sha256=_ZoG8snICK2bidWtc2KOGs738LWg9_r66V9mOMnEb-E,71
 aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/__init__.py,sha256=-fAORvyFmG2iSvFOFDixmt9OTQRR58y89uhhu2EgbA8,46
-aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=-IwTmcZFlgUzxxHgcaR9jmbVKCP3IFEHtqzAD4pek6s,200
-aiagents4pharma/talk2biomodels/__init__.py,sha256=9MuyHb5KTf5ufeyq7fu5xoLEwVT688DFOWuKuzdWG9o,140
+aiagents4pharma/configs/talk2biomodels/agents/t2b_agent/default.yaml,sha256=yD7qZCneaM-JE5PdZjDmDoTRUdsFrzeCKZsBx1b-f20,293
+aiagents4pharma/talk2biomodels/__init__.py,sha256=qUw3qXrENqSCLIKSLy_qtNPwPDTb1wdZ8fZispcHb3g,141
 aiagents4pharma/talk2biomodels/agents/__init__.py,sha256=sn5-fREjMdEvb-OUan3iOqrgYGjplNx3J8hYOaW0Po8,128
 aiagents4pharma/talk2biomodels/agents/t2b_agent.py,sha256=nVWxHR-QMZDqDwxvDga_CvLo7LHP5cWCDl6lXCMcRO0,3264
 aiagents4pharma/talk2biomodels/models/__init__.py,sha256=5fTHHm3PVloYPNKXbgNlcPgv3-u28ZquxGydFYDfhJA,122
 aiagents4pharma/talk2biomodels/models/basico_model.py,sha256=js7ORLwbJPaIsko5oRToMMCh4l8LsN292OIvFzTfvRg,4946
 aiagents4pharma/talk2biomodels/models/sys_bio_model.py,sha256=ylpPba2SA8kl68q3k1kJbiUdRYplPHykyslTQLDZ19I,1995
 aiagents4pharma/talk2biomodels/states/__init__.py,sha256=YLg1-N0D9qyRRLRqwqfLCLAqZYDtMVZTfI8Y0b_4tbA,139
-aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=cneAsNgtzDoL3_gkC4gf7h69BfBOY7rASpYWz4I8jjI,761
+aiagents4pharma/talk2biomodels/states/state_talk2biomodels.py,sha256=iob7q5Kpy6aWDLCiFsp4NNVYYXNdDU3vU50PmxyvBsU,792
 aiagents4pharma/talk2biomodels/tests/__init__.py,sha256=Jbw5tJxSrjGoaK5IX3pJWDCNzhrVQ10lkYq2oQ_KQD8,45
 aiagents4pharma/talk2biomodels/tests/test_basico_model.py,sha256=uqhbojcA4RRTDRUAF9B9DzKCo3OOIOWMDK8IViG0gsM,2038
-aiagents4pharma/talk2biomodels/tests/test_langgraph.py,sha256=z3bS_LE2s9kba2fFM5SWQy1uIalQBbCnGJuakQjnKTQ,7365
+aiagents4pharma/talk2biomodels/tests/test_langgraph.py,sha256=GyqsUpcWgjuRb15DpGvLg-FZ8g3_cf0TwVcaCPp_vO0,9456
 aiagents4pharma/talk2biomodels/tests/test_sys_bio_model.py,sha256=nA6bRT16627mw8qzrv7cHM9AByHb9F0kxAuwOpE-avA,1961
 aiagents4pharma/talk2biomodels/tools/__init__.py,sha256=8hAT6z1OO8N9HRylh6fwoqyjYlGdpkngkElBNqH40Zo,237
-aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=UEdT46DIFZHlAOF4cNX4_s7VjHvbbiGpNmEY2-XW2iA,2655
-aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=BfLSivWqtRVZDeqD7RP5sgZP6B9rET47IWdNrA3gmIE,3825
-aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=czxjRa9jvjTow-POGU5wSV8_lwfknAezBnzCFA0gQ8E,5189
+aiagents4pharma/talk2biomodels/tools/ask_question.py,sha256=uxCQ4ON8--D0ACPvT14t6x_aqm9LP6woBA4GM7bPXc4,3061
+aiagents4pharma/talk2biomodels/tools/custom_plotter.py,sha256=HWwKTX3o4dk0GcRVTO2hPrFSu98mtJ4TKC_hbHXOe1c,4018
+aiagents4pharma/talk2biomodels/tools/get_modelinfo.py,sha256=68KmeEpgvgaDQM9airOWVy4fGT33rG10RlXhps5W6C0,5279
 aiagents4pharma/talk2biomodels/tools/load_biomodel.py,sha256=pyVzLQoMnuJYEwsjeOlqcUrbU1F1Z-pNlgkhFaoKpy0,689
 aiagents4pharma/talk2biomodels/tools/search_models.py,sha256=Iq2ddofOOfZYtAurCISq3bAq5rbwB3l_rL1lgEFyFCI,2653
-aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=hBRrSLVGcaT157FCe8ajVKJZ2fi9CJhGeniGLaZJ-KE,6251
+aiagents4pharma/talk2biomodels/tools/simulate_model.py,sha256=1HVoI5SkktvpOmTnAG8hxrhpoxpg_he-bb5ZJ_UllI4,6833
 aiagents4pharma/talk2cells/__init__.py,sha256=zmOP5RAhabgKIQP-W4P4qKME2tG3fhAXM3MeO5_H8kE,120
 aiagents4pharma/talk2cells/agents/__init__.py,sha256=38nK2a_lEFRjO3qD6Fo9a3983ZCYat6hmJKWY61y2Mo,128
 aiagents4pharma/talk2cells/agents/scp_agent.py,sha256=gDMfhUNWHa_XWOqm1Ql6yLAdI_7bnIk5sRYn43H2sYk,3090
@@ -55,8 +55,8 @@ aiagents4pharma/talk2knowledgegraphs/utils/embeddings/__init__.py,sha256=xRb0x7S
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/embeddings.py,sha256=1nGznrAj-xT0xuSMBGz2dOujJ7M_IwSR84njxtxsy9A,2523
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/huggingface.py,sha256=2vi_elf6EgzfagFAO5QnL3a_aXZyN7B1EBziu44MTfM,3806
 aiagents4pharma/talk2knowledgegraphs/utils/embeddings/sentence_transformer.py,sha256=36iKlisOpMtGR5xfTAlSHXWvPqVC_Jbezod8kbBBMVg,2136
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